Deep Learning Based Biomedical NER Framework

Robert Phan; Thoai Man Luu; Rachel Davey; Girija Chetty

doi:10.1109/SSCI.2018.8628740

Deep Learning Based Biomedical NER Framework

Robert Phan, Thoai Man Luu, Rachel Davey, Girija Chetty

Research output: A Conference proceeding or a Chapter in Book › Conference contribution › peer-review

4 Citations (Scopus)

Abstract

This paper describes a novel deep learning-based framework for biomedical name entity recognition. Bio-Entity name entity recognition task based on three different deep learning techniques: Feedforward Networks (FFNs), Recurrent Neural Networks (RNNs), and Hybrid Convolutional Neural Networks (CNNs), has allowed better latent feature learning and discovery for the complex NLP task. The performance evaluation of the proposed framework with the BioNLP dataset corresponding to biomedical entity recognition task, has led to promising performance, when assessed in terms of F-measure, Recall and Precision. The best performing deep learner based on Hybrid CNN approach has resulted in an F-score of 70.32%, and surpassed the performance reported by other participants in the Challenge task.

Original language	English
Title of host publication	Proceedings of the 2018 IEEE Symposium Series on Computational Intelligence, SSCI 2018
Editors	Suresh Sundaram
Place of Publication	Bangalore, India
Publisher	IEEE, Institute of Electrical and Electronics Engineers
Pages	33-40
Number of pages	8
ISBN (Electronic)	9781538692769
ISBN (Print)	9781538692769
DOIs	https://doi.org/10.1109/SSCI.2018.8628740
Publication status	Published - 18 Nov 2018
Event	2018 IEEE Symposium Series on Computational Intelligence - Sheraton Grand Bangalore Hotel, Bengalore, India Duration: 18 Nov 2018 → 21 Nov 2018 http://ieee-ssci2018.org/

Publication series

Name	Proceedings of the 2018 IEEE Symposium Series on Computational Intelligence, SSCI 2018

Conference

Conference	2018 IEEE Symposium Series on Computational Intelligence
Abbreviated title	IEEE-SSCI 2018
Country/Territory	India
City	Bengalore
Period	18/11/18 → 21/11/18
Internet address	http://ieee-ssci2018.org/

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10.1109/SSCI.2018.8628740

Cite this

Phan, R., Luu, T. M., Davey, R., & Chetty, G. (2018). Deep Learning Based Biomedical NER Framework. In S. Sundaram (Ed.), Proceedings of the 2018 IEEE Symposium Series on Computational Intelligence, SSCI 2018 (pp. 33-40). [8628740] (Proceedings of the 2018 IEEE Symposium Series on Computational Intelligence, SSCI 2018). IEEE, Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/SSCI.2018.8628740

Phan, Robert ; Luu, Thoai Man ; Davey, Rachel et al. / Deep Learning Based Biomedical NER Framework. Proceedings of the 2018 IEEE Symposium Series on Computational Intelligence, SSCI 2018. editor / Suresh Sundaram. Bangalore, India : IEEE, Institute of Electrical and Electronics Engineers, 2018. pp. 33-40 (Proceedings of the 2018 IEEE Symposium Series on Computational Intelligence, SSCI 2018).

@inproceedings{ec8958121dd04f07966be12690b2c54a,

title = "Deep Learning Based Biomedical NER Framework",

abstract = "This paper describes a novel deep learning-based framework for biomedical name entity recognition. Bio-Entity name entity recognition task based on three different deep learning techniques: Feedforward Networks (FFNs), Recurrent Neural Networks (RNNs), and Hybrid Convolutional Neural Networks (CNNs), has allowed better latent feature learning and discovery for the complex NLP task. The performance evaluation of the proposed framework with the BioNLP dataset corresponding to biomedical entity recognition task, has led to promising performance, when assessed in terms of F-measure, Recall and Precision. The best performing deep learner based on Hybrid CNN approach has resulted in an F-score of 70.32%, and surpassed the performance reported by other participants in the Challenge task.",

keywords = "convolutional neural networks, deep learning, feedforward networks, machine learning, optimization algorithm, recurrent neural networks",

author = "Robert Phan and Luu, {Thoai Man} and Rachel Davey and Girija Chetty",

year = "2018",

month = nov,

day = "18",

doi = "10.1109/SSCI.2018.8628740",

language = "English",

isbn = "9781538692769",

series = "Proceedings of the 2018 IEEE Symposium Series on Computational Intelligence, SSCI 2018",

publisher = "IEEE, Institute of Electrical and Electronics Engineers",

pages = "33--40",

editor = "Suresh Sundaram",

booktitle = "Proceedings of the 2018 IEEE Symposium Series on Computational Intelligence, SSCI 2018",

address = "United States",

note = "2018 IEEE Symposium Series on Computational Intelligence, IEEE-SSCI 2018 ; Conference date: 18-11-2018 Through 21-11-2018",

url = "http://ieee-ssci2018.org/",

}

Phan, R, Luu, TM, Davey, R & Chetty, G 2018, Deep Learning Based Biomedical NER Framework. in S Sundaram (ed.), Proceedings of the 2018 IEEE Symposium Series on Computational Intelligence, SSCI 2018., 8628740, Proceedings of the 2018 IEEE Symposium Series on Computational Intelligence, SSCI 2018, IEEE, Institute of Electrical and Electronics Engineers, Bangalore, India, pp. 33-40, 2018 IEEE Symposium Series on Computational Intelligence, Bengalore, India, 18/11/18. https://doi.org/10.1109/SSCI.2018.8628740

Deep Learning Based Biomedical NER Framework. / Phan, Robert; Luu, Thoai Man; Davey, Rachel et al.
Proceedings of the 2018 IEEE Symposium Series on Computational Intelligence, SSCI 2018. ed. / Suresh Sundaram. Bangalore, India: IEEE, Institute of Electrical and Electronics Engineers, 2018. p. 33-40 8628740 (Proceedings of the 2018 IEEE Symposium Series on Computational Intelligence, SSCI 2018).

Research output: A Conference proceeding or a Chapter in Book › Conference contribution › peer-review

TY - GEN

T1 - Deep Learning Based Biomedical NER Framework

AU - Phan, Robert

AU - Luu, Thoai Man

AU - Davey, Rachel

AU - Chetty, Girija

PY - 2018/11/18

Y1 - 2018/11/18

N2 - This paper describes a novel deep learning-based framework for biomedical name entity recognition. Bio-Entity name entity recognition task based on three different deep learning techniques: Feedforward Networks (FFNs), Recurrent Neural Networks (RNNs), and Hybrid Convolutional Neural Networks (CNNs), has allowed better latent feature learning and discovery for the complex NLP task. The performance evaluation of the proposed framework with the BioNLP dataset corresponding to biomedical entity recognition task, has led to promising performance, when assessed in terms of F-measure, Recall and Precision. The best performing deep learner based on Hybrid CNN approach has resulted in an F-score of 70.32%, and surpassed the performance reported by other participants in the Challenge task.

AB - This paper describes a novel deep learning-based framework for biomedical name entity recognition. Bio-Entity name entity recognition task based on three different deep learning techniques: Feedforward Networks (FFNs), Recurrent Neural Networks (RNNs), and Hybrid Convolutional Neural Networks (CNNs), has allowed better latent feature learning and discovery for the complex NLP task. The performance evaluation of the proposed framework with the BioNLP dataset corresponding to biomedical entity recognition task, has led to promising performance, when assessed in terms of F-measure, Recall and Precision. The best performing deep learner based on Hybrid CNN approach has resulted in an F-score of 70.32%, and surpassed the performance reported by other participants in the Challenge task.

KW - convolutional neural networks

KW - deep learning

KW - feedforward networks

KW - machine learning

KW - optimization algorithm

KW - recurrent neural networks

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DO - 10.1109/SSCI.2018.8628740

M3 - Conference contribution

SN - 9781538692769

T3 - Proceedings of the 2018 IEEE Symposium Series on Computational Intelligence, SSCI 2018

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BT - Proceedings of the 2018 IEEE Symposium Series on Computational Intelligence, SSCI 2018

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Phan R, Luu TM, Davey R , Chetty G. Deep Learning Based Biomedical NER Framework. In Sundaram S, editor, Proceedings of the 2018 IEEE Symposium Series on Computational Intelligence, SSCI 2018. Bangalore, India: IEEE, Institute of Electrical and Electronics Engineers. 2018. p. 33-40. 8628740. (Proceedings of the 2018 IEEE Symposium Series on Computational Intelligence, SSCI 2018). doi: 10.1109/SSCI.2018.8628740

Deep Learning Based Biomedical NER Framework

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